title: Dynamic chromatin regulatory landscape of human CAR T cell exhaustion [HiChIP]

city: Stanford

first: David

middle: G

last: Gennert

address: 269 Campus Drive

department: Genetics

institute: Stanford University School of Medicine

summary: Dysfunction in T cells limits the efficacy of cancer immunotherapy. We profiled the epigenome, transcriptome, and enhancer connectome of exhaustion-prone GD2-targeting HA-28z chimeric antigen receptor (CAR) T cells and control CD19-targeting CAR T cells, which present less exhaustion-inducing tonic signaling, at multiple points during their ex vivo expansion. We found widespread, dynamic changes in chromatin accessibility and 3D chromosome conformation preceding changes in gene expression, notably at loci proximal to exhaustion-associated genes such as PDCD1, CTLA4, and HAVCR2, and increased DNA motif access for AP-1 family transcription factors, which are known to promote exhaustion. Although T cell exhaustion has been studied in detail in mouse, we find that the regulatory networks of T cell exhaustion differ between the species and involve distinct loci of accessible chromatin and cis-regulated target genes in human CAR T cell exhaustion. Deletion of exhaustion-specific candidate enhancers of PDCD1 suppress the expression of PD-1 in an in vitro model of T cell dysfunction and in HA-28z CAR T cells, suggesting enhancer editing as a path forward in improving cancer immunotherapy.

overall_design: HiChIP profiles of H3K27ac-associated chromosome loops in primary T cells (“Day 0”) and CAR T cells expressing either the CD19_28z or HA_28z CAR at Day 10 were generated by sequencing on the Illumina NextSeq.  T cells were first sorted for CD8+ and naïve surface marker expression and processed in duplicate.

first: Maxwell

last: Mumbach

first: Jeffrey

last: Granja

first: Rachel

last: Lynn

first: Evan

last: Weber

first: Ansuman

middle: T

last: Satpaty

first: Crystal

last: Mackall

first: Howard

middle: Y

last: Chang


title: Dynamic chromatin regulatory landscape of human CAR T cell exhaustion [ATAC-seq]

status: Public on May 01 2021

state: CA

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ATAC_seq profiles of primary T cells ("Day 0") and CAR T cells expressing either the CD19_28z or HA_28z CAR at Days 7 and 14 were generated by sequencing on the Illumina NextSeq.  CAR T cells were first sorted by CD4+/CD8+ expression and Naïve/Central Memory surface marker expression and processed in duplicate.

middle: M

middle: C

middle: W

middle: L


title: Linking the FTO obesity rs1421085 variant circuitry to cellular, metabolic and organismal phenotypes in vivo

city: Oxford

first: Michelle

last: Simon

address: Harwell Innovation Center

department: Bioinformatics

country: United Kingdom

institute: Medical Research Council

summary: Atac-seq in iWAT pre-adipocytes at day 1 of adipogenic induction

first: Sam

last: Laber


title: RNA-sequencing of 14 diverse mouse strains treated with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

type: Expression profiling by high throughput sequencing

summary: The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor in the PAS superfamily of environmental sensors that is linked to several metabolic diseases, including non-alcoholic fatty liver disease (NAFLD). Much remains unknown regarding the impact of genetic variation in AHR-driven disease, as past studies have focused on a small number of inbred strains. Recently, the presence of a wide-range of interindividual variability amongst humans was reported in response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the prototypical ligand of the AHR. In this study, a panel of 14 diverse mouse strains were exposed to TCDD for 10 days to characterize the AHR-mediated response across genetic backgrounds. In this study, responses to TCDD are heavily-dependent on genetic background. While mice carry one of four Ahr alleles that impact the AHR-mediated responses, we observed significant intra-allelic variability suggesting the presence of novel genetic modifiers of AHR signaling. A regression-based approach was used to scan for genes regulated by the AHR and/or associated with TCDD-induced phenotypes. The approach identified seven genes, 2 of which are novel, that are likely regulated by the AHR based on association with hepatic TCDD burden (p≤0.05). Finally, we identified a gene, Dio1, which was associated with change in percent body fat across the diverse set of strains (p≤0.05). Overall, the results in this study exemplify the power of genetics-based approaches in identifying novel genes that are putatively regulated by the AHR.

overall_design: Females were checked daily for vaginal plugs. If a plug was present, mice were separated, weighed, and randomly placed into vehicle or TCDD dose groups. TCDD was administered to mice using peanut butter as the vehicle daily for 10 consecutive days . On day 11, mice were anesthetized with avertin, euthanized via CO2 asphyxiation, and tissues were snap frozen in liquid nitrogen. Pregnancy success was assessed by the presence of absorption sites or embryos within the uterus under a dissection microscope; only pregnant mice were included in downstream analysis.

first: Amanda

last: Jurgelwicz

first: Peter

last: Dornbos

first: Melanie

last: Warren

first: Anooj

last: Arkatar

first: Hui

last: Lin

last: Threadgill

first: Tim

middle: R

last: Zacharewski

first: John

middle: J

last: LaPres


title: RNA-seq analysis of rat cardiac fibroblast transcriptome at three distinct developmental ages

city: Medford

first: Lauren

middle: D

last: Black III

state: MA

address: 4 Colby Street

department: Biomedical Engineering

institute: Tufts University

summary: The purpose of this study was to map the cardiac fibroblast transcriptome at three distinct developmental ages to investigate age-dependent gene expression differences in these cells, which are critically important to extracellular matrix turnover and repair, the inflammatory process, and cardiac remodeling after injury. To do so we isolated RNA from Sprague Dawley rats at fetal, neonatal, and adult developmental stages and performed RNA-seq. Overall, we identified an array of transcriptomic differences with respect to developmental age that suggests that CFs increase expression of immune- and inflammation-associated genes with age, with a decrease in cardiac development-associated genes and pathways. These results reinforce established evidence of phenotypic heternogenity of CFs with respect to age.

overall_design: Rat (Sprague Dawley) fetal (E18), neonatal (P1), and adult (7 week old) cardiac fibroblast RNA comparative analysis.

first: Luke

last: Perreault

first: Thanh

last: Le

first: Madeleine

last: Oudin

last: Black II


title: Universal Toxicity Gene Signatures for Early Identification of Drug-induced Tissue Injuries in Rats

city: West Point

first: Keith

last: Tanis

address: 770 Sumnetown Pike

institute: Merck & Co, Inc

summary: A new safety testing paradigm that relies on gene expression biomarker panels was developed that can easily and quickly identify dose-dependent drug-induced injuries across a number of different tissues in rats prior to drug candidate selection. The resource-sparing approach has yielded positive impact on early compound de-risking, enabling drug advancement in a cost-effective manner while reducing later probability of attrition. Here we describe the development, qualification, and implementation of gene expression signatures that diagnose tissue degeneration/necrosis for use in an early rat Safety Lead Optimization (SLO) tolerability study or other early exploratory rat study conducted to assess drug action. Microarray data were used to first identify approximately 400 differentially expressed genes that were discovered as being shared consistently across 4 prioritized tissues (liver, kidney, heart, and skeletal muscle), following injuries induced by known toxicants and so were termed ‘universal’.   Quantitative PCR on ~100 of those genes followed, and the approach was extended across 4 other tissues (pancreas, 5 sections of the gastrointestinal tract (GI), bladder, and testes) where acute toxicities are historically less common. The most consistent and robustly responding transcripts were selected, resulting in a final 22-gene set (16 universal genes and 6 tissue-specific genes) from which unique sets of 12 genes were chosen as optimal for each of 8 tissues. Mathematical algorithms were generated to convert each tissue's gene expression fold change values for the 12 genes to a single metric, scaled between 0 and 1, and a positive threshold set. For liver, kidney, heart, and skeletal muscle, this was established using a training set of 22 compounds and the performance determined by testing a set of approximately 100 additional rat studies resulting in approximately 90% sensitivity and 100% specificity. Similar performance was observed across a more limited set of 15 studies for pancreas, GI, bladder, and testes. Bundled together, we have incorporated these gene expression signature panels into a 4 day rat SLO toxicity study design, which provides a rapid objective assessment of more commonly seen compound liabilities, benchmarks non-toxic and toxic doses and exposures, and guides selection of lead candidates to reduce attrition without the necessity to perform time-consuming tissue and slide preparation, and expert microscopic histopathologic analyses, which can be reserved for advancing more optimized compounds at later development stages.

overall_design: Compilation of multiple different studies (TT#'s) of various design in liver, kidney, skeletal muscle and heart as indicated in the metadata.

middle: Q

first: Warren

middle: E

last: Glaab

first: Daniel

middle: H

last: Holder

first: Yudong

last: He

first: Wendy

last: Bailey

first: David

last: Gerhold

first: Carolann

last: Beare

first: Zoltan

last: Erdos

first: Pamala

last: Lane

first: Laura

last: Michna

first: Nagaraja

last: Muniapppa

first: Jeffery

last: Laurence

first: Joseph

middle: F

last: Sina

first: Thomas

last: Skopek

first: Farnk

last: Sistare


title: Cardiomyocyte heterogeneity in zebrafish development and regeneration

status: Public on May 03 2021

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Contrary to adult mammals, zebrafish are able to regenerate their heart after cardiac injury.  This regenerative response relies, in part, on the endogenous ability of cardiomyocytes (CMs) to dedifferentiate and proliferate to replenish the lost muscle.  However, CM heterogeneity and population dynamics during development and regeneration remain poorly understood.  Through comparative transcriptomic analyses of the developing and adult zebrafish heart, we identified tnnc2 and tnni4b.3 expression as markers for CMs at early and late developmental stages, respectively.  Using newly developed reporter lines for these genes, we investigated their expression dynamics during development and regeneration, and observed interesting expression patterns.  tnnc2 reporter lines label most CMs at embryonic stages, and this labeling declines rapidly during larval stages; in adult hearts expression is only detectable in a subset of CMs.  Conversely, expression of a tnni4b.3 reporter is initially visible in outer curvature CMs at larval stages, and it is subsequently present in a vast majority of the CMs in adult hearts.  Interestingly, we find that the adult CMs labeled by the embryonic reporter display higher levels of Tg(tp1:EGFP) expression, which indicates active Notch signaling.  To further characterize this CM population, we performed transcriptomic analysis and found that it expresses genes encoding components of the Notch signaling pathway as well as markers of immature CMs.  Moreover, during heart regeneration, proliferating CMs in the injured area activate the embryonic CM reporter.  Overall, our findings provide further evidence of cardiomyocyte heterogeneity in the adult zebrafish heart.

overall_design: Total RNA was isolated from sorted myl7:EGFP+ (7000 cells) and tp1:EGFP+/myl7:DsRed2-NLS+ (2000 cells).  In both cases, RNA was extracted using RNeasy Micro Kit (Qiagen) following manufacturer’s instructions.

first: Ayele

last: Taddese Tsedeke

first: Srinivas

last: Allanki

first: Vanesa

last: Jimenez-Amilburu

last: Guenther

first: Shih-Lei

last: Lai

first: Didier

last: Stainier

first: Rubén

last: Marín-Juez


title: Dynamic chromatin regulatory landscape of human CAR T cell exhaustion

first: David

last: Gennert

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: FcγR engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity

status: Public on Apr 30 2021

city: Boston

first: Tanya

last: Mayadas

address: 77 Avenue Louis Pasteur

department: Department of Pathology

institute: Brigham and Women's Hospital

summary: Classical dendritic cells (cDC) are professional antigen presenting cells (APC) that regulate immunity and tolerance. Neutrophil-derived cells with properties of DCs (nAPC) are observed after culture of neutrophils with cytokines and in human diseases. Here, we show that FcgR-mediated endocytosis of antigen-antibody complexes or an anti-FcgRIIIB-antigen conjugate converts neutrophils into nAPCs that, in contrast to those generated with cytokines alone, activate T cells to levels observed with cDCs and elicit CD8 T cell-dependent anti-tumor immunity. Single cell transcript analyses and validation studies implicate the transcription factor PU.1 in neutrophil to nAPC conversion. In humans, nAPC frequency in lupus patient blood containing IgG-immune complexes correlates with disease. Moreover, conjugate treatment of neutrophils from individuals with myeloid neoplasms that harbor neoantigens or those who are vaccinated against bacterial toxins generates nAPCs that activate autologous T cells. Thus, anti-FcgRIIIB-antigen conjugate-induced conversion of neutrophils to immunogenic nAPCs may represent a new immunotherapy for cancer and infectious diseases.

overall_design: i) Sorted splenic Ly6G+CD11c+/-MHCII+/- cells isolated from three FcγR humanized mice after treatment with 3G8-conjugate, ii) neutrophils cultured in vitro with 3G8-conjugate and collected at day 0, 1, 2, and 3, and iii) splenic cells from untreated wild-type mice and FcγR humanized mice.

first: Vijayashree

last: Mysore

last: Mears


title: Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine

city: Durham

first: Gilberto

last: Padilla Mercado

state: NC

address: 213 Research Drive 327 CARL Building

department: Molecular Genetics & Microbiology

institute: Duke University

summary: The purpose of this study was to elucidate potential effects of fxr mutation on the functional specification of intestinal epithelial cells. To do this, we sorted GFP-positive cells from TgBAC(cldn15la:GFP) transgenics of either fxr+/+ or fxr-/- fish larvae and subjected them to 10X Genomics single-cell RNA-seq. Our results uncovered the requirement of fxr in gene expression and differentiation among multiple intestinal epithelial cell types.

overall_design: Analysis of sorted cells from 6 days post-fertilization zebrafish larvae that were either fxr+/+ (WT) or fxr-/- (MUT)

first: Jia

last: Wen

middle: P

last: Mercado

first: Alyssa

last: Volland

first: Heidi

last: Doden

first: Colin

last: Lickwar

first: Taylor

last: Crooks

first: Genta

last: Kakiyama

first: Cecelia

last: Kelly

first: Jordan

last: Cocchiaro

first: Jason

last: Ridlon

first: John

last: Rawls


title: Transcriptome-based identification of the beneficial role of blackcurrant, strawberry and yellow onion to attenuate the cytopathic effects of Clostridium difficile toxins

city: Wageningen

first: Nicole

last: de Wit

address: Bornse Weilanden 9

department: Food & Biobased Research

country: Netherlands

institute: Wageningen UR

summary: Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of food compounds on (intestinal) health. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were incubated with in vitro digested onion extracts for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify onion-induced gene expression profiles in Caco-2 cells, digested yellow onion and white onion samples were compared to a digest control samples. Results: We found that yellow onion (n=5586, p<0.05) had a more pronounced effect on gene expression than white onion (n=3688, p<0.05). However, a substantial number of genes (n=3281, p<0.05) were affected by both onion variants in the same direction. Pathway analyses revealed that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions. Our data fit with previous in vivo studies showing that the beneficial effects of onions are mostly linked to their antioxidant properties. Conclusion: our data indicate that the in vitro Caco-2 intestinal model can be used to determine modes of action of nutritional compounds and can thereby reduce the number of animals used in conventional nutritional intervention studies.

overall_design: Microarray analysis was performed on 21-days differentiated Caco-2 cells incubated with C. Difficile Toxin A (ToxA), Toxin B (ToxB), Toxin A + Toxin B (ToxAB), Toxoid A + Toxoid B (Toxoid AB) or DMEM (= control medium) for ~4 hours. This experiment was performed three times, so three independent biological replicates per treatment were included in the microarray analysis.

first: Prashanna

last: Venkatasubramanian

first: Edoardo

last: Saccenti

first: Jurriaan

last: Mes


title: Non-deletional CD8+ T cell self-tolerance permits responsiveness but limits tissue damage

city: Minneapolis

first: Todd

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Self-specific CD8+ T cells often escape clonal deletion, but the properties and capabilities of such cells in a physiological setting are unclear. We characterized polyclonal CD8+ T cells specific for the melanocyte antigen tyrosinase-related protein 2 (Trp2) in mice that express or lack this enzyme due to deficiency in Dct, which encodes Trp2. The size, phenotype, and gene expression profile of the pre-immune Trp2/Kb-specific pool were similar in wild-type (WT) and Dct-deficient (Dct-/-) mice. Despite comparable initial responses to Trp2 immunization, WT Trp2/Kb-specific cells showed blunted expansion, and scRNAseq revealed WT cells less readily differentiated into a CD25+ proliferative population. Functional self-tolerance clearly emerged when assessing immunopathology: adoptively transferred WT Trp2/Kb-specific cells mediated vitiligo much less efficiently. Hence, CD8+ T cell self-specificity is poorly predicted by precursor frequency, phenotype or even initial responsiveness, while deficient activation-induced CD25 expression and other gene expression characteristics may help to identify functionally tolerant cells.

overall_design: Comparison of tolerant (WT) versus non-tolerant (KO or Dct-/-) CD8+ Trp2-specific cells. Number, phenotype, expansion, and functionality were compared. This analysis included gene expression comparisons between Trp2-specific cells from WT vs. KO/Dct-/- naive mice (bulk RNAseq in pre-immune mice) and mice treated with TriVax 3 or 7 days prior (single cell [sc] RNAseq).

first: Emily

middle: N

last: Truckenbrod

first: Kristina

middle: S

last: Burrack

first: Henrique

last: Borges da Silva

first: Katharine

last: Block

first: Katie

last: Stagliano

first: Arthur

middle: A

last: Hurwitz

first: Ross

middle: B

last: Fulton

first: Kristin

last: Renkema

first: Stephen

last: Jameson


title: Novel Role for Macrophage Galactose-type Lectin-1 to Regulate Innate Immunity against Mycobacterium tuberculosis

city: Galveston

first: Kubra

last: Naqvi

state: TX

address: 301 University blvd

institute: University of Texas Medical Branch

summary: Tuberculosis (TB) caused by infection with Mycobacterium tuberculosis (Mtb) is characterized by inflammatory pathology and poorly understood mechanisms of innate immunity. Pattern recognition receptors (PRR), expressed on the surface of macrophages, determine the balance of inflammatory and antimicrobial functions that influence disease outcome. Carbohydrate moieties displayed by mycobacteria can serve as PRR ligands for some members of the C-type lectin receptor (CLR) family; interactions that mediate a variety of incompletely understood immune outcomes. This work identifies a novel role for the CLR Macrophage Galactose-type Lectin-1 (MGL-1) in a mouse model of experimental tuberculosis. Murine macrophages upregulated MGL-1 following in vitro exposure to Mtb, while MGL+ cells accumulated at sites of mycobacteria-driven inflammation in the lung. Pulmonary macrophages from MGL-1-deficient mice displayed increased production of pro-inflammatory cytokines (IL-1b, IL-6 and IFN-g) that was associated with greater lipid accumulation, following Mtb infection. Surprisingly for a CLR, we also observed MGL-1-dependent anti-mycobacterial activity as evidenced by greater Mtb proliferation in BMDM, and the lung, of MGL-1 deficient mice. These results identify MGL-1 signaling as an important mechanism that regulates innate immunity against Mtb and indicate potential for the MGL pathway as a novel therapeutic target for anti-TB immunity.

overall_design:
Next Generation Sequencing of WT (MGL-1+/+) ( n=5) versus MGL-1-/- (n=5) at 2 and 8 weeks post-Mtb infection or uninfected. Sequencing was performed on lung tissue RNA.
The strain used for this study is B6.129-Clec10atm1Hed/J from Jackson labs and WT littermates.

first: Matthew

last: Huante

first: Tais

last: Saito

first: Mark

last: Endsley

first: Benjamin

last: Gelman

first: Janice


title: Long-term impact of placental allopregnanolone insufficiency on the mouse transcriptome of cerebral cortex, hippocampus, hypothalamus and cerebellum

status: Public on Apr 28 2021

city: NEW YORK

first: Claire-Marie

last: Vacher

state: NY

address: 630 West 168th Street

department: Pediatrics

institute: Columbia University

summary:
Goal: To test the long-term influence of placental allopregnanolone (ALLO) loss on mouse brain transcriptome, in a sex- and region-specficic manner.
Methods: We deleted the gene encoding the synthetic enzyme for ALLO (Akr1c14) specifically in trophoblasts by crossing Akr1c14-floxed mice with Cyp19a-Cre mice (plKO mice). Region-specific mRNA profiles of 30-day old WT and plKO mice were generated by 3'mRNA sequencing, in triplicate, using Illumina HiSeq 2500.
Results: Our RNA sequencing analysis reveals that placental ALLO withdrawal is associated with region- and sex-specific gene expression changes. The differentially expressed genes are notably associated with myelination and autism spectrum disorders.
Conclusions: We show that placental ALLO insufficiency is associated with long-term changes in gene expression in the mouse brain in a sex- and region-specific manner.

first: Anna

last: Penn

first: Yuka

last: Imamura Kawasawa

first: Toru

last: Sasaki

first: Kazue

last: Hashimoto-Torii


title: The abaI/abaR quorum sensing system effects pathogenicity in Acinetobacter baumannii

city: Changchun

first: Xiaoyu

last: Sun

address: Xinmin street

country: China

institute: Jilin university

summary: Acinetobacter baumannii is a Gram-negative pathogen that has emerged as one of the most troublesome pathogens for health care institutions globally. Bacterial quorum sensing (QS) is a process of cell-to-cell communication that relies on the production, secretion and detection of autoinducer (AI) signals to share information about cell density and regulate gene expression accordingly. The molecular and genetic basis of Acinetobacter baumannii virulence remains poorly understood. Therefore, the contribution of the abaI/abaR quorum sensing system to growth characteristics, morphology, biofilm formation, resistance, motility and virulence of Acinetobacter baumannii was studied in detail. RNA-seq analysis indicated that genes involved in various aspects of energy production and conversion, Valine, leucine and isoleucine degradation and lipid transport and metabolism are associated with bacterial pathogenicity. Our work provides a new insight into abaI/abaR quorum sensing system effects pathogenicity in A. baumannii. We propose that targeting the AHL synthase enzyme abaI could provide an effective strategy for attenuating virulence. On the contrary, interdicting the autoinducer synthase–receptor abaR elicits unpredictable consequences, which may lead to enhanced bacterial virulence.

overall_design: WT, ΔabaI, ΔabaR and ΔabaIR

first: Zhaohui

last: Ni

first: Fan

last: Li


title: Metabolomics and Transcriptomics Reveal Key Metabolism Pathways of Giant Embryo Development in Rice

status: Public on Apr 27 2021

city: Shanghai

first: Zejun

last: Hu

address: Yangpu District Songhu Road No. 2005

institute: Fudan University

summary: Rice embryos are rich in high-quality protein, fat, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, map-based cloning, metabolomics, and transcriptomics were applied to explore the giant embryo rice cultivar Dapeimi grown under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of GE, and the functional mutation site is a single cytosine deletion in the exon1, which differed from the findings of previous reports. The identification and analysis of differential metabolites indicated that plants lacking the GE mainly promoted amino acid metabolism, energy metabolism, and lipid metabolism pathways in the rice embryo. Changes of gene expression in related metabolic regulatory networks were analyzed, and substantial changes in the transcriptome supported the metabolomics results. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for improving rice nutrition and breeding high-nutrition varieties.

overall_design: embryo mRNA profiles of 15-day old NIL-D (EG) and NIL-X (CG) were generated by deep sequencing in triplicates

first: Qiangqiang

last: Xiong

first: Kai

last: Wang

first: Lixia

last: Zhang

first: Ying

last: Yan

first: Liming

last: Cao

first: Fuan

last: Niu

first: Jinyan

last: Zhu

first: Jinlong

first: Shujun

last: Wu


title: Cytokine-enhanced cytolytic activity of Exosomes from NK Cells [small RNA seq]

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: LMSCGR

institute: NIAMS/NIH

type: Non-coding RNA profiling by high throughput sequencing

summary: Natural killer (NK) cells are a type of innate lymphocytes that play key roles in immune surveillance against tumors and viral infection. NK cells distinguish abnormal cells from healthy cells by cell-cell interaction with cell surface proteins and then attack target cells via multiple mechanisms involving TRAIL, Fas Ligand, cytokine secretion, perforin, and granzymes. In addition, extracellular vesicles (EVs), including exosomes derived from NK cells (NK-EVs), possess cytotoxic capacity against tumor cells, but their characteristics and regulation by cytokines remain unknown. Here, we report that EVs derived from human NK-92 cells stimulated with IL-15 + IL-21 show enhanced cytotoxic capacity against tumor cells in a granzyme B independent manner. In addition, small RNA-seq and mass spectrometry analyses indicate that miRNA and protein profiles in EVs are altered by cytokine stimulation. We also show NK-EVs are taken up by target cells via macropinocytosis. Collectively, our findings reveal novel characteristics of NK-EVs and the mechanism of their incorporation into target cells.

overall_design: 24 samples

first: Yutaka

last: Enomoto

first: Dimitrios

middle: G

last: Anastasakis

first: Warren

last: Leonard


title: Transcriptional profile of planarian FACS populations at different nutritional status

status: Public on Apr 26 2021

city: Jena

first: Oscar

middle: Gutierrez

last: Gutierrez

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: We performed RNA-seq of X1, X2 and Xins subfractions at 1 day of starvation (1dS), 7days of starvation (7dS) and 30days of starvation (30dS)

overall_design: The overall aim of this work was to characterize the transcriptional profile of stem cells (X1) at different nutritional status.

first: Óscar

last: Gutiérrez-Gutiérrez

first: Cristina

last: González-Estévez


title: Targeting IRF7 asthma phenotypes through immuno-modulation therapy

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

summary: Viral-induced severe asthma exacerbations in children are characterized by IRF7hi and IRF7lo molecular phenotypes. We have developed an experimental animal model that mirrors these response patterns in asthma-resistant PVG and asthma-susceptible BN rats respectively. We aimed to i) characterize the immunological and molecular hallmarks of PVG and BN responses to virus/allergen exposure, and (ii) evaluate the utility of innate immune training with the bacterial lysate OM85 to attenuate ensuing inflammation.  Animals were sensitized to OVA/alum, inoculated with murine-adapted Rhinovirus model (vMC0), and challenged with OVA 24h later. RNA-seq was performed on lung and bone marrow at several time points post virus/allergen exposure.

overall_design: 191 samples in total: 95 lung samples (48 from BN, 47 from PVG) and 96 bone marrow samples (47 from BN, 49 from PVG). Aprox half of samples are from untreated animals, the other half from OM-85 treated animals. Within each strain, tissue and treatment group, samples are further divided into four experimental groups (with n=5-7); group 1 = no OVA or virus, group 2 = no OVA with virus 1 day post infection (DPI), group 3 = OVA and virus 2 DPI, group 4 = OVA and virus 9 DPI)

first: Jeff

last: Lauzon-Joset

first: Anthony

last: Bosco


title: Stage-specific transcriptomic changes in α-cells after massive β-cell loss

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

summary: Conversion of α-cells into insulin-producers upon β-cell loss is modulated by constitutive signals ensuring α-cell identity maintenance. Here, we characterized the plasticity of mouse α-cells by profiling their transcriptome at different time-points after massive β-cell ablation. Our results show that α-cells undergo stage-specific transcriptional changes 5- and 15-days post-diphtheria toxin (DT)-mediated β-cell ablation. At 5 days, α-cells transiently upregulate various genes associated with interferon signaling and proliferation, including Interferon Induced Protein with Tetratricopeptide Repeats 3 (Ifit3). Subsequently, at 15 days post β-cell ablation, α-cells undergo a transient downregulation of genes from several pathways including Insulin receptor, mTOR and MET signaling. These results pinpoint novel markers discriminating α-cells at different stages after acute β-cell loss, and highlight additional signaling pathways that could be involved in reprogramming the functional identity of α-cells.

overall_design: α-cell transcriptional profile upon β-cell loss.

first: Daniel

last: Oropeza

first: Valentina

last: Cigliola

first: Agustín

last: Romero

first: Simona

last: Chera

last: Rodríguez-Seguí

first: Pedro

last: Herrera


title: Host-pathogen interaction of Atlantic salmon (Salmo salar) and the ectoparasite, Neoparamoeba perurans in amoebic gill disease

city: St Lucia

first: Natasha

last: Botwright

state: QLD

address: 306 Carmody Road

department: Agriculture and Food

institute: CSIRO

summary: Marine farmed Atlantic salmon (Salmo salar) are repeatedly susceptible to amoebic gill disease (AGD) caused by the ectoparasite Neoparamoeba perurans over their life cycle. The parasite elicits a highly localized response within the gill epithelium mucosa resulting in multifocal mucoid patches at the site of parasite attachment. This host-pathogen response drives a complex immune reaction within the pathology of the disease, which remains poorly understood. A dual RNA-seq approach was employed using Illumina sequencing technology to investigate both the linteraction between the host and the parasite.

sample_organism:
Salmo salar
Paramoeba perurans

platform_organism:
Salmo salar
Paramoeba perurans

overall_design: A multi-tissue transcriptomic data set was generated from the gill (including both lesioned and non-lesioned tissue), head kidney and spleen tissues of AGD unaffected (n=4) and affected Atlantic salmon (n=4).

first: Amin

last: Mohamed

first: Joel

last: Slinger

first: Paula

last: Lima

first: James

middle: W

last: Wynne


title: Single-cell RNA-seq following APE1/Ref-1 knockdown in Pancreatic Ductal Adenocarcinoma

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

summary: APE1 was knocked down using siRNA in low passage patient-derived PDAC cells and the resulting cells, along with control cells were analysed using scRNA-seq to identify differentially expressed genes and pathways as a result of APE1 knock-down.

overall_design: siRNA APE1 knock-down versus scrambled control, The SMARTer system was used to generate cDNA from 96 captured single cells. Unstranded 2x100bp reads were sequenced using a HiSeq2500 on rapid run mode in 1 lane.


title: Role of Ikaros in the transcriptional signature of Th17 cells

city: Illkirch

first: Celine

last: Charvet

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

country: France

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

summary: We found that CD4+ T cells require Ikaros to promote IL-17 production when cultured in Th17 conditions. To understand why Ikaros null T cells do not produce IL-17, we analyzed the transcriptome of WT vs. Ikaros null naive CD4+ T cells both resting (day 0) or activated with anti-CD3 plus anti-CD28 antibodies, IL-6, TGFb1 and neutralizing anti-IFNg and anti-IL-4 antibodies (Th17 condition) for 1 or 2 days. Samples from 3 independent experiments were analyzed.

overall_design:
3 independent experiments were performed

Purified naive CD4+ T cells (CD4+CD8-CD44loCD62L+CD25-) from spleen of Ikarosf/f (WT) or Ikarosf/f x CD4-Cre (TKO) mice (6-7 weeks-old) were activated on a plate, pretreated with Goat anti-Hamster IgG and coated with anti-CD3 (2C11; 1 µg/ml) and anti-CD28 (37.51; 0.25µg/ml) Abs, in the presence of mIL-6 (20 ng/ml), hTGFb1 (1 ng/ml) and neutralizing anti-IL-4 and anti-IFNg Abs (2 µg/ml each). RNA from cells cultured for 1 and 2 days as well as with naive CD4+ T cells (day 0) was extracted and used for a transcriptome analysis using GeneChip® Mouse Gene 2.0ST arrays (Affymetrix).

first: Chiara

last: Bernardi

first: Gaëtan

last: Maurer

first: Patricia

last: Marchal

first: Philippe

last: Kastner

first: Susan

last: Chan

first: Céline


title: T cell response to CD200+/- acute myeloid leukemia

status: Public on Apr 24 2021

city: Houston

first: Shelley

last: Herbrich

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary:
Purpose: Understanding immunosuppression in AML is critical . The goals of this study are to compare the transcriptomics of human CD3+ T cells from humanized mice exposed to CD200+/- AML.
Methods:  NSG mice were humanized with 10x10^6 healthy PBMCs prior to the introduction of CD200+ or CD200- OCI-AML3 cells. After 10 days, CD3+ T cells were isolated and RNA was sequenced.
Results: T cells from mice with CD200+ AML were characterized  by an enrichment of T cell activation pathways and a downregulation of numerous metabolic pathways, including OXPHOS and glycolysis.
Conclusions:  Our results demonstrate, for the first time, that CD200+ AML can directly impair T cell metbolism.

overall_design: RNA-seq analysis of sorted CD3+ human T cells extracted from PBMC-humanized mice with either CD200+ (n=3), CD200- (n=3) OCI-AML3 leukemia, or controls (n=2). Results provide insight into the mechanisms of CD200 immunosuppression.

first: Marina

last: Konopleva


title: Putative Genes Identified in Alkaloid Biosynthesis in Dendrobium officinale by Correlating the Contents of Main Bioactive Metabolites with Genes Expression between Protocorm-like Bodies and Leaves

city: Hefei

first: Shihai

last: Xing

state: Anhui

address: No.1 Qianjiang Road, Xinzhan District

institute: Anhui University of Chinese Medicine

summary:
Background: Dendrobium officinale, an endangered Chinese herb, has extensive therapeutic effects and contains bioactive ingredients including a large number of polysaccharides and alkaloids, and minimal flavonoids. Firstly, this study attempts to obtain the protocorm-like bodies of this plant through tissue culture to produce the main secondary metabolites whose distribution in each organelle and protocorm like bodies is analyzed. Then, analysis of the correlation between comparative transcriptome sequence and the metabolite content in different organs enables the discovery of putative genes encoding enzymes involved in the biosynthesis of polysaccharides and alkaloids, and flavonoids.
Results: The optimum condition for protocorm-like bodies (PLBs) induction and propagation of D. officinale is established. For protocorm induction, we use the seed as the explant, and the optimum medium formula for PLBs propagation is 1/2 MS + α-NAA 0.5 mg·L-1 +6-BA 1.0 mg·L-1 + 2, 4-D 1.5-2.0 mg·L-1 + potato juice 100 g·L-1. The distribution of polysaccharides, alkaloids and flavonoids in D. officinale organs was clarified. Stems, PLBs and leaves have the highest content of polysaccharides, alkaloids and flavonoids, respectively. PLBs replace organs to produce alkaloids in D. officinale, and naringenin was only produced in stem. Hot water extraction (HWE) method was found outperforming the ultrasound-assisted extraction (UAE) method for polysaccharides from D. officinale. A comparative transcriptome analysis of the protocorm-like bodies and leaves of D. officinale showed genes encoding enzymes involved in polysaccharides, alkaloids and flavonoids biosynthetic pathway were differentially expressed. Putative genes encoding enzymes involved in polysaccharides, alkaloids and flavonoids synthetic pathway were identified. Notably, genes encoding enzymes of strictosidine beta-glucosidase, geissoschizine synthase and vinorine synthase in alkaloids biosynthesis of D. officinale are first reported.
Conclusions: Our works, especially the identification of candidate genes encoding enzymes involved in metabolites biosynthesis will help to explore and protect the endangered genetic resources and will also facilitate further analysis of the molecular mechanism of secondary metabolites’ biosynthesis in D. officinale.

overall_design: This study aimed to establish a system for protocorm, PLB induction and proliferation for Dendrobium officinale. We compared the contents of main metabolites in PLBs and organs from the original plant. Transcriptome sequencing was used to analyze expression levels of genes encoding candidate enzymes that are involved in the biosynthesis pathway of these specific metabolites in leaves and PLBs.

first: Zhaojian

last: Wang


title: Exosomal miRNAs differences analysis between C26 and MC38

first: chunxiao

last: miao

state: Shanghai

address: Shanghai, China

institute: Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine

summary: MiRNAs contained in C26-derived and MC38-derived exosomes were determined by IlluminaHiSeq platform. High-throughput sequencing was conducted at Shanghai MajorbioBiopharm TechnologyCo., Ltd. (Shanghai, China). In brief, total RNA from exosomes was prepared and quantified with a NanoDrop ND-2000(NanoDrop Technologies).RNA integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies,Santa Clara, CA, USA). A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Small RNA adapters were then ligated to the 5’ and 3’ ends of total RNA. After cDNA synthesis and amplification, the PCR-amplified fragments were purified from the PAGE gel, and the completed cDNA libraries were quantified by an Agilent 2100 Bioanalyzer. Cluster generation was performed on an IlluminacBot, and sequencing was performed on an IlluminaHiSeq 2000 platform and 50bp single-end reads were generated.The expression level of each miRNA was calculated according to the transcripts per million reads (TPM) method. Significant differently expressed (DE) miRNAs were extracted with |log2FC|>1 and FDR < 0.05 by DEseq2.

overall_design: Exosomes were extracted from conditioned medium of C26 and MC38 cells. MiRNAs contained in C26-derived and MC38-derived exosomes were determined by IlluminaHiSeq platform.

first: Chunxiao

last: Miao

first: Wanli

last: Zhang

first: Lixing

last: Feng

first: Xiongwen


title: ATAC-seq from foreskin keratinocyte (ENCSR247PVM)

status: Public on Apr 22 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ATAC-seq on primary keratinocytes in day 1.5 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR158XTU)

summary:
ATAC-seq on primary keratinocytes in day 2.5 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR677MJF)

summary:
ATAC-seq on primary keratinocytes in day 0.5 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR923WGJ)

summary:
ATAC-seq on primary keratinocytes in day 4.5 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR356KRQ)

summary:
ATAC-seq on primary keratinocytes in day 0.0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR649RCV)

summary:
ATAC-seq on primary keratinocytes in day 5.5 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR939WVU)

summary:
ATAC-seq on primary keratinocytes in day 5.0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR460DKJ)

summary:
ATAC-seq on primary keratinocytes in day 3.5 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR290YMN)

summary:
ATAC-seq on primary keratinocytes in day 1.0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR572UDP)

summary:
ATAC-seq on primary keratinocytes in day 2.0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptomics of Zinc-limited and Zinc-replete Mycobacterium tuberculosis

status: Public on Apr 21 2021

city: Honolulu

first: Sladjana

last: Prisic

state: HI

address: 1800 East-West Rd

institute: University of Hawaii

summary: Mycobacterium tuberculosis H37Rv (Mtb) was grown in Sauton's medium with and without added zinc. Cultures were grown for 10 days and RNA was harvested from TRIzol extractions.

overall_design: Transcriptomes of Mtb grown in zinc-replete and zinc-limited medium.

first: Allexa

last: Dow


title: Gene Expression profile for the characterization of PD-L1 blockade in melanoma model

status: Public on Apr 20 2021

city: bethesda

first: abdalla

last: abdelmaksoud

state: maryland

address: 37 Convent Dr

institute: NCI

summary: Only a subset of patients responds to immune checkpoint blockade in melanoma. A preclinical model recapitulating the clinical activity of ICB would provide a valuable platform for mechanistic studies. We used melanoma tumors arising from an Hgftg;Cdk4R24C/R24C genetically engineered mouse (GEM) model to evaluate the efficacy of an anti-mouse PD-L1 antibody similar to the anti-human PD-L1 antibodies durvalumab and atezolizumab. Consistent with clinical observations for ICB in melanoma, anti-PD-L1 treatment elicited complete and durable response in a subset of melanoma-bearing mice. We also observed tumor growth delay or regression followed by recurrence.  For early treatment assessment, we analyzed gene expression profiles, T cell infiltration, and T cell receptor (TCR) signatures in regressing tumors compared to tumors exhibiting no response to anti-PD-L1 treatment. We found that CD8+ T cell tumor infiltration corresponded to response to treatment, and that anti-PD-L1 gene signature response indicated an increase in antigen processing and presentation, cytokine-cytokine receptor interaction, and natural killer cell-mediated cytotoxicity. TCR sequence data suggest that an anti-PD-L1-mediated melanoma regression response requires not only an expansion of the TCR repertoire that is unique to individual mice, but also tumor access to the appropriate TCRs. Thus, this melanoma model recapitulated the variable response to ICB observed in patients and exhibited biomarkers that differentiate between early response and resistance to treatment, providing a valuable platform for prediction of successful immunotherapy.

overall_design: Mice were treated with anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS at 10mg/kg or 20mg/kg intraperitoneally twice weekly for a maximum of 6 doses over 3 weeks in the initial efficacy study, or over a longer period to assess tumor response as indicated in the text. For each study the vehicle control group received PBS (10ml/kg) and an additional antibody control group received mouse IgG1 D265A (AstraZeneca clone: Cat# NIP228, Batch# SP16-017) in PBS at 10 or 20mg/kg. Tumor growth was monitored by caliper measurement. Tumors were harvested from treated mice at several different endpoints (delayed growth, stabilization, regression) or when they reached a maximum tumor volume of 2000 mm3. At necropsy, tumors were divided into sections for fixation or flash-freezing. Blood samples were taken from each mouse prior to treatment and at the time of tumor harvest.     To evaluate response in biomarker studies (Study 2 or 3), tumors from mice treated with anti-PD-L1 were harvested after 2-12 doses based on regression in tumor volume after two consecutive measurements (Responders). Anti-PD-L1-treated tumors that exhibited growth progression were harvested at matching timepoints (Non-responders). Tumors that regressed to below measurable volumes after initial treatment but regrew after 4-10 doses of anti-PD-L1 were also harvested (Relapse). PBS- and control IgG-treated tumors were also harvested at multiple time points for comparison. Additionally, any mice that did not experience initial tumor growth, but developed tumors after anti-PD-L1 treatment were designated as Growth Delay. Any tumor that decreased in volume by 5% or more was designated as a Responder. Within the Responder group, tumors with no volume change between 2 consecutive measurements were designated as growth stabilization.

first: Rajaa

last: El Meskini

first: Devon

last: Atkinson

first: Alan

last: Kulaga

first: Abdalla

last: Abdelmaksoud

first: Susana

last: Hayes

first: Zoë

last: Ohler


title: FER-regulated genes under moderate intensity light

city: DAEJEON

first: Hyo-Jun

last: Lee

state: DAEJEON

address: 125 GWAHAK-RO YUSEONG-GU

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Col-0 and fer-4 seedlings grown for 7 d under moderate intensity light (150 PFD) were used for RNA-sequencing

overall_design: Three biological replicates for Col-0 and fer-4 samples were analyzed. Control: Col-0

first: Seung

middle: Y

last: Shin

first: Ji-Sun

last: Park

first: Hye-Bin

first: Hyun-Soon

last: Kim

first: Jae-Heung

last: Jeon

first: Hye

last: Cho


title: Host transcriptome response to SARS-CoV2 infection

status: Public on Apr 16 2021

city: Duarte

first: Guihua

last: Sun

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

summary: HEK293T stable express hACE2 was infected by SARS-CoV-2 (WA1) and RNA-seq was performed to profile host gene expression in response to SARS-COV-2 infection

overall_design: Both mock and infection samples were duplicated, infected at MOI=1 for three days

first: Yanhong

last: Shi

first: Vaithilingaraja

last: Arumugaswami

first: Arthur

last: Riggs


title: ATAC-seq from foreskin keratinocyte (ENCSR798IJQ)

first: ENCODE

last: DCC

summary:
ATAC-seq on primary keratinocytes in day 6.0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: A unified atlas of CD8 T cell dysfunctional states in cancer and infection

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: CD8 T cells play an essential role in defense against viral and bacterial infections and in tumor immunity. Deciphering T cell loss of functionality is complicated by the conspicuous heterogeneity of CD8 T cell states described across different experimental and clinical settings. By carrying out a unified analysis of over 300 ATAC-seq and RNA-seq experiments from twelve independent studies of CD8 T cell dysfunction in cancer and infection we defined a shared differentiation trajectory towards terminal dysfunction and its underlying transcriptional drivers and revealed a universal early bifurcation of functional and dysfunctional T cell activation states across models. Experimental dissection of acute and chronic viral infection using scATAC-seq and allele-specific scRNA-seq identified state-specific transcription factors and captured the early emergence of highly similar TCF1+ progenitor-like populations at an early branch point, at which epigenetic features of functional and dysfunctional T cells diverge. Our atlas of CD8 T cell states will facilitate mechanistic studies of T cell immunity and translational efforts.

overall_design: scATAC-seq, scRNA-seq, CUT&RUN in CD8 T cells from LCMV Armstrong or Clone 13 infected mice

first: Joris

last: van der Veeken

first: Alexander

last: Rudensky

first: Christina

last: Leslie


title: Expression data from wild type, CBFB-MYH11-overexpressing,  DNMT3A knockdown and RUNX1 knockdown K562 cells

status: Public on Apr 13 2021

first: Peng

last: Liu

address: Dong An Road, 131

institute: Fudan University

summary: We searched for genes which are mutated in a manner that is linked with gene mutations involved in DNA de/methylation in AML. We found that recurrent CBFB-MYH11 fusions, which result in the expression of fusion protein comprising core-binding factor β (CBFB) and myosin heavy chain 11 (MYH11), occur mutually exclusively with DNMT3A mutations. The CBFB-MYH11 fusion tumors show DNA hypomethylation patterns similar to cancers with loss-of-function mutation of DNMT3A. Expression of CBFB-MYH11 fusion protein or inhibition of DNMT3A similarly impairs the methylation and expression of target genes of Runt related transcription factor 1 (RUNX1), a functional partner of CBFB. We demonstrate that RUNX1 directly interacts with DNMT3A and that CBFB-MYH11 fusion protein sequesters RUNX1 in the cytoplasm, thereby preventing RUNX1 from interacting with and recruiting DNMT3A to its target genes. Our results identify a novel regulation of DNA methylation and provide a molecular basis how CBFB-MYH11 fusion contributes to leukemogenesis.

overall_design: mRNA profiles of overexpression of plvx-vector/flag-CBFB-MYH11 fusion protein in K562 cells. And mRNA profiles of Knockdown of DNMT3A/RUNX1 in K562 cells as well as control K562 cells(PLKO). Expression levels of genes as well as repetitive elements were investigated.

first: Jin-Pin

first: Si-Jia

first: Yun

last: Gao

first: Ying-Jie

last: Ai

first: Xiu-Fei

last: Chen

first: Yi-Ping

first: Kun-Liang

last: Guan

first: Yue

last: Xiong

first: Hai-Xin

last: Yuan


title: ATAC-seq from foreskin keratinocyte (ENCSR245LNF)

state: CA

summary:
ATAC-seq on primary keratinocytes in day 3.0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from foreskin keratinocyte (ENCSR521RAL)

summary:
ATAC-seq on primary keratinocytes in day 4.0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Different gene expression profiles of granulosa cells in Chinese obese patients with or without polycystic ovary syndrome

status: Public on Apr 14 2021

city: Wuhan

first: Ruxing

last: Wu

state: Hubei

address: No.1095 Jie Fang Avenue, Hankou, Wuhan,Hubei, China.

department: Obstetrics and Gynecology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Obese or polycystic ovary syndrome (PCOS) women have encountered poor reproductive outcomes in natural as well as assisted conception. Furthermore, pregnancy complications of women with PCOS are profoundly worsened by obesity. Both obesity and PCOS affect function of granulosa cells, which is essential in offering the oocyte with nutrients and growth regulators.

overall_design: Sixteen patients who had undergone in vitro fertility (IVF) or intracytoplasmic sperm injection (ICSI) were enrolled in the study: 8 obese patients—4 none-PCOS(NPO) and 4 PCOS (PO); 8 normal weight patients—4 none-PCOS(NPN) and 4 PCOS (PN). Seven binary comparisons were as follows: (i) NPO/NPN, (ii)PO/PN, (iii) O/N, (iv) PN/NPN, (v) PO/NPO, (vi)P/NP,(vii) PO/NPN.

first: RuXing

first: XiaoYuan

last: Huang

first: HanWang

last: Zhang


title: Transcriptome sequencing of Paracoccus denitrificans ATCC19367 with florfenicol exporsure

city: Guangzhou

first: Mei

last: Wang

state: Guangdong

address: 483 Wushan Road

department: College of Veterinary Medicine

institute: South China Agricultural University

summary: We report the application of transcriptome sequencing technology in florfenicol interfering with denitrification by Paracoccus denitrificans. More than 30 billion bases of sequences were obtained by sequencing analysis. We found 433 differentially expressed genes, of which 292 genes were down-regulated and 141 genes were up-regulated, respectively. Importantly, most of the denitrification genes were suppressed, which further led to the enrichment of key metabolic pathways. The weakening of protein synthesis was consistent with the bacteriostatic mechanism of florfenicol. In particular, we found 42 putative differentially expressed sRNAs. After homologous alignment, target gene prediction and functional analysis, it was proved that the sRNAs differential expression profile is likely to be a key transcription factor affected by antibiotics in denitrification. This study provides new ideas for further control of environmental antibiotic pollution.

overall_design: Transcriptome detection of Paracoccus denitrificans ATCC19367 with or without florfenicol exporsure.

first: Tong

last: Zhou

first: Yi

last: Liang

first: Ganwu

last: Li

first: Yongxue

last: Sun


title: Multi-omics profiling of living human pancreatic islet donors reveals heterogeneous beta cell trajectories toward type 2 diabetes

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: To gain insight into the history of islet cell deterioration along the progression from normal glycemic regulation to T2D, we collected surgical pancreatic tissue samples from 133 metabolically phenotyped pancreatectomized patients (PPP). Gene expression profiles of islets isolated by laser capture microdissection (LCM) from resected and snap-frozen pancreas samples were assessed by RNA sequencing.

overall_design:
This study includes RNA-Seq samples from pancreatic islets of 133 human donors, stratified into four groups based on their diabetes status: 18 were non-diabetic (ND), 41 had impaired glucose tolerance (IGT), 35 had Type 3c diabetes (T3cD), and 39 had Type 2 diabetes (T2D). The group assignments are based on thresholds defined in the guidelines of the American Diabetes Association.

For data analysis, a subset of 92 pancreatic islet samples was defined, which included only those samples in which the gene INS showed the highest expression (i.e., highest normalized counts value). Statistical analyses were performed both on the complete transcriptomics data set and on this restricted data set.

first: Marko

last: Barovic

first: Andreas

last: Brunner

first: Matthias

last: Mann

first: Mark

last: Ibberson

first: Michele

last: Solimena


title: Single cell transcriptome atlases of the developing mouse and human spinal cord

status: Public on Apr 12 2021

city: London

first: James

last: Briscoe

address: 1 Midland Road

institute: The Francis Crick Institute

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of Scots pine seedlings

status: Public on Apr 15 2021

city: Oulu

first: Janne

last: Koskimäki

address: Pentti Kaiteran katu 1

department: Ecology and Genetics Research Unit

country: Finland

institute: University of Oulu

summary: The meristem-associated endosymbiont M. extorquens DSM13060 significantly increases needle and root growth of Scots pine (Pinus sylvestris L.) seedlings without producing plant hormones, but by aggregating around host nuclei. Here we studied gene expression of the pine host induced by M. extorquens DSM13060 infection. We selected the time point of 90 days post-inoculation for our analysis based, because at this point, Methylorubrum extorquens DSM13060 has systemically colonized the pine seedlings, being found throughout tissues of roots and shoots.

overall_design: Analysis used total RNA of the untreated pine seedlings as control samples for comparison to the experimental samples, seedlings inoculated with M. extorquens DSM13060, harvested at 90 days post-inoculation. cDNAs of the treatment/control were hybridized with custom microarray chips in total of six times (n=6) with two-color dye-swap approach to minimize technical variability and dye bias.

first: Jouni

last: Kvist

first: Silvia

last: Fluch

first: Anna

middle: M

last: Pirttilä


title: Single cell transcriptome atlases of the developing mouse and human spinal cord [mouse dataset]

first: Christopher

last: Barrington

state: London

address: Midland Road

institute: Francis Crick Institute

summary: The spinal cord receives input from peripheral sensory neurons and controls motor output by regulating muscle innervating motor neurons. These functions are carried out by neural circuits comprising molecularly and physiologically distinct neuronal subtypes that are generated in a characteristic spatial-temporal arrangement from progenitors in the embryonic neural tube. The systematic mapping of gene expression in mouse embryos has provided insight into the diversity and complexity of cells in the neural tube. For human embryos, however, less information has been available. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions in four human embryos of Carnegie Stages (CS) CS12, CS14, CS17 and CS19 from Gestational Weeks (W) 4-7. In total we recovered the transcriptomes of 71,219 cells. Analysis of progenitor and neuronal populations from the neural tube, as well as cells of the peripheral nervous system, in dorsal root ganglia adjacent to the neural tube, identified dozens of distinct cell types and facilitated the reconstruction of the differentiation pathways of specific neuronal subtypes. Comparison with existing mouse datasets revealed the overall similarity of mouse and human neural tube development while highlighting specific features that differed between species. These data provide a catalogue of gene expression and cell type identity in the developing neural tube that will support future studies of sensory and motor control systems.

overall_design: Three independent mouse embryos were dissected and processed together to obtain a concentration of cells similar to the other mouse datasets. These were separated into two biological replicates from which scRNA-seq libraries were prepared.

first: Teresa

last: Rayon

first: Rory

middle: J

last: Maizels


title: Single cell transcriptome atlases of the developing mouse and human spinal cord [human dataset]

overall_design: Four time points of human development are sampled (CS12, CS14, CS17, CS19). Where possible, tissue was dissected into brachial and thoracic samples and further separated into biological replicates where enough cells were available.


title: Homeostatic function of monocyte and interstitial lung macrophages are regulated via collagen binding domain receptor LAIR1.

city: South San Francisco

first: Yasin

last: Senbabaoglu

state: California

address: 1 DNA Way

institute: Genentech


title: Homeostatic function of monocyte and interstitial lung macrophages are regulated via collagen binding domain receptor LAIR1 (scRNAseq)

summary:
Monocytes and macrophages play pivotal roles in tissue homeostasis and tumor progression. Here, we show that these cells express high levels of LAIR1, a known receptor for Collagen. Using a high throughput cell-based platform for interactome discovery, we identified Colec12, a protein expressed by stromal cells, as a novel high affinity LAIR1 ligand. Using a combination of genomic, phenotypic, global phosphoproteomics and transcriptomics assays, we corroborated the role of LAIR1 signaling in myeloid cells. Under homeostasis LAIR1 restrained proliferation and promoted survival of non-classical monocytes and dysregulation of this pathway led to an increase in classical monocytes and tissue-infiltrating macrophages in lungs. In tumors, LAIR1 deficiency in myeloid cells exacerbated metastasis to lungs and confirmed LAIR1 as a positive prognostic factor in human metastatic melanoma. Our study shows extracellular matrix provides monocytes and lung interstitial macrophages important homeostatic signals that are mediated via LAIR1.
Methods: 10x single cell RNA sequencing was performed to characterize the differences between WT and LAIR1KO lung myeloid cells with and without tumor. Murine lungs were digested, cells were hashtagged and FACS-sorted for Interstitial macrophages, Alveolar macrophages, classical and nonclassical monocytes.

overall_design: Examination of 3 hashtagged replicates from WT normal, LAIR1KO normal, B16/F10-bearing WT , and B16/F10-bearing LAIR1KO murine lungs

first: Shilpa

last: Keerthivasan

first: Nadia

last: Martinez

first: Shannon

last: Turley


title: Homeostatic function of monocyte and interstitial lung macrophages are regulated via collagen binding domain receptor LAIR1 (bulk RNAseq)

summary:
Background:  We observed that LAIR1 is highly expressed in murine nonclassical monocytes. This study aims to understand gene expression differences between LAIR1-/- and LAIR1+/+  murine bone marrow nonclassical monocytes.
Methods: Ly6C- nonclassical monocytes were sorted out of murine bone marrows and harvested for RNA-seq.

overall_design: Examination of 5 replicates from WT and LAIR1KO nonclassical monocytes


title: Long noncoding RNA MIR4435-2HG enhances metabolic function of myeloid dendritic cells from HIV-1 elite controllers (RNAseq)

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

summary: Restriction of HIV-1 replication in elite controllers (ECs) is frequently attributed to T cell-mediated immune responses, while the specific contribution of innate immune cells is less clear. Here, we demonstrated an upregulation of the host long non-coding RNA (lncRNA) MIR4435-2HG in primary myeloid dendritic cells (mDc) from ECs. Elevated expression of this lncRNA in mDCs was associated with a distinct immunometabolic profile, characterized by increased oxidative phosphorylation and glycolysis activities in response to TLR3 stimulation. Using functional assays, we showed that MIR4435-2HG directly influenced the metabolic state of mDCs, likely through epigenetic mechanisms involving H3K27ac enrichment at an intronic enhancer in the RPTOR gene locus, the main component of the mammalian target of rapamycin complex 1 (mTORC1). Together, these results suggested a role of MIR4435-2HG for enhancing immunometabolic activities of mDCs in ECs through targeted epigenetic modifications of a member of the mTOR signaling pathway.

overall_design: We performed RNAseq on MIR4435-2HG silenced and Poly(I:C)-stimulated myeloid DCs from PBMCs of five HIV-1 negative individuals to prolife the gene expression.

first: Ciputra

last: Hartana

first: Yelizaveta

last: Rassadkina

first: Enrique

last: Martin-Gayo

first: Bruce

middle: D

last: Walker

first: Mathias

last: Lichterfeld

first: Xu

last: Yu


title: Role of rsc2 in nucleotide excision repair in yeast

city: Pullman

first: John

middle: J.

last: Wyrick

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: Nucleosomes are a significant barrier to the repair of UV damage because they impede damage recognition by nucleotide excision repair (NER). The RSC chromatin remodeler functions in cells to promote DNA access by moving or evicting nucleosomes and has been linked to NER in yeast. Here, we report genome-wide repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast cells lacking Rsc2.

overall_design: UV-induced CPD lesions were mapped in yeast cells both Immediately after UV damage formation (0hr time point) and following two hours of repair (2hr time point) using the CPD-seq method. Repair of CPD lesions was measured in yeast cells mutated for the rsc2 subunit of the RSC ATP-dependent chromatin remodeling complex.

first: Kaitlynne

last: Bohm


title: Single-cell Transcriptome of Bronchoalveolar Lavage Fluid Reveals Dynamic Change of Macrophages During SARS-CoV-2 Infection in Ferrets

status: Public on Apr 11 2021

city: Daejeon

first: Kijong

last: Yi

state: Daejeon

address: 291 Daehak-ro, #N26

department: Graduate School of Medical Science and Engineering

institute: Korea Advanced Institute of Science and Technology

summary: Single-cell transcriptome of bronchoalveolar lavage fluid cells longitudinally obtained from SARS-CoV-2-infected ferrets was analyzed. Changes in cell proportions and characteristics in uninfected control, at 2 days post-infection (dpi), and 5 dpi were noted. Macrophages were classified into the subpopulations with dynamic changes quantitatively and qualitatively over time. Fundamental aspects of the immune response dynamics provoked by SARS-CoV-2 infection were highlighted in this study.

overall_design: Total 10 single cell RNA seq libraries (10X Chromium, v3) were sequenced. All samples are bronchoalveolar lavage fluid cells from ferret. Samples are consist with 3 control (healthy) ferrets, 3 ferrets at 2 dpi of SARS-CoV-2, and 4 ferrets of 5 dpi.

first: Jeong Seok

last: Lee

first: June-Young

last: Koh

first: Young-Il

last: Kim

first: Su-Jin

last: Park

first: Eun-Ha

first: Se-Mi

first: Sung Ho

first: Young Seok

last: Ju

first: Young Ki

last: Choi

first: Su-Hyung


title: RSC chromatin remodeler regulates base excision repair of MMS induced DNA damage

summary: Nucleosomes are a significant barrier to the repair of UV damage because they impede damage recognition by nucleotide excision repair (NER). The RSC and SWI/SNF chromatin remodelers function in cells to promote DNA access by moving or evicting nucleosomes and both have been linked to NER in yeast. Here, we report genome-wide repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast cells lacking RSC or SWI/SNF activity. Our data indicate that SWI/SNF is not generally required for NER, but instead promotes repair of CPD lesions at specific yeast genes. In contrast, mutation or depletion of RSC subunits causes a general defect in NER across the yeast genome. Our data indicate that RSC is required for repair not only in nucleosomal DNA, but also neighboring linker DNA and nucleosome-free regions (NFRs). Intriguingly, while depletion of the RSC catalytic subunit also affects base excision repair (BER) of N-methylpurine (NMP) lesions, RSC activity is less important for BER in linker DNA and NFRs. Furthermore, our data indicate that RSC plays a direct role in transcription coupled-NER (TC-NER) of transcribed DNA. These findings help to define the specific genomic and chromatin contexts in which each chromatin remodeler functions in DNA repair, and indicate that RSC plays a unique function in facilitating repair by both NER subpathways.

overall_design: Genome-wide mapping of MMS lesion repair using the N-methylpurine-sequencing (NMP-seq) in wild-type (WT-AA) or Sth1-anchor away (Sth1-AA) yeast strains treated with rapamycin.


title: FVE directly enriches to RdDM target loci.

status: Public on Apr 10 2021

city: Shanghai

first: Pei

last: Huang

address: Fenglin Road 300

institute: Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai

summary: Using ChIP-seq to study the deposition of FVE on the chromatin

overall_design: Examination of FVE enrichment on the chromatin using ChIP-seq

first: Huan

first: Xueqiang

last: Lin

first: Pan

last: Liu

first: Lun

last: Zhao

first: Wenfeng

last: Nie

first: Zhaobo

last: Lang

first: Jian-Kang

last: Zhu


title: FVE regulates DNA methylation levels at a subset of RdDM loci.

type: Methylation profiling by high throughput sequencing

summary: Using BS-Seq to provide single-base resolution of DNA methylation status in Col-0 WT, nrpd1-3, nrpe1-11 and fve-4.

overall_design: BS-Seq: Col-0 WT and mutants (nrpd1-3, nrpe1-11 and fve-4)


title: FVE affects 24-nt siRNA accumulation downstream of RdDM pathway

summary: Using siRNA-Seq to provide siRNA accumulation status in fve mutant.

overall_design: Examination of siRNA accumulation in Col-0 WT and fve-4 mutant using siRNA-seq


title: RNA-seq data for E2F6 knockdown in Huh7 cells

first: Jing

middle: tian

last: tian

address: Dongchuan Road

institute: Shanghai Jiaotong University

summary: E2F6 plays oncogenic roles and in order to identify the molecular mechanism of E2F6 to promote tumorigenesis, RNA-seq was performed on Huh7 cells with or without E2F6.

overall_design: Huh7 cell  were transfected with E2F6 shRNA. After E2F6 was knocked down, total RNA was isolated and subjected to RNA-seq.

first: Tiantian

last: Jing

first: Yongzhong


title: RNA-seq data for USP22 knockdown in Huh7 cells

summary: USP22 plays oncogenic roles and in order to identify the molecular mechanism of USP22 to promote tumorigenesis, RNA-seq was performed on Huh7 cells with or without USP22.

overall_design: Huh7 cell  were transfected with USP22 shRNA. After USP22 was knocked down, total RNA was isolated and subjected to RNA-seq.


title: Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates

status: Public on Apr 07 2021

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin


title: Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [RNA-seq]

summary: We used RNA-Seq to measure transcript abundance in 15 Saccharomyces cerevisiae strains from a diverse range of genetic lineages when growing in rich media (YPD) to characterize differential expression across strains.

overall_design: RNA-seq and transcriptome analysis of BY4743 and 14 wild S. cerevisiae isolates. Three biological replicate cell samples (collected on different days) were harvested for RNASeq analysis. Cells were grown in YPD for at least three generations to log phase (OD600 ~0.5) and collected by centrifugation.

first: DeElegant

last: Robinson


title: Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regualtion

status: Public on Apr 08 2021

city: Bristol

first: Benjamin

last: Flynn

state: County (optional)

address: Dorothy Hodgkin Building, Whitson street

institute: University of Bristol

summary: Ultradian glucocorticoid rhythms are highly conserved across mammalian species, however, their functional significance is not yet fully understood. Here we demonstrate that pulsatile corticosterone replacement in adrenalectomised rats induces a dynamic pattern of glucocorticoid receptor (GR) binding at ~3,000 genomic sites in liver at the pulse peak, subsequently not found during the pulse nadir. In contrast, constant corticosterone replacement induced prolonged binding at the majority of these sites. Additionally, each pattern further induced markedly different transcriptional responses. During pulsatile treatment, intragenic occupancy by active RNA polymerase II exhibited pulsatile dynamics with transient changes in enrichment, either decreased or increased depending on the gene, which mostly returned to baseline during the inter-pulse interval. In contrast, constant corticosterone exposure induced prolonged effects on RNA polymerase II occupancy at the majority of gene targets, thus acting as a sustained regulatory signal for both transactivation and repression of glucocorticoid target genes. The nett effect of these differences were consequently seen in the liver transcriptome as RNA-seq analysis indicated that despite the same overall amount of corticosterone infused, twice the number of transcripts were regulated by constant corticosterone infusion, when compared to pulsatile. Target genes that were found to be differentially regulated in a pattern-dependent manner were enriched in functional pathways including carbohydrate, cholesterol, glucose and fat metabolism as well as inflammation, suggesting a functional role for dysregulated glucocorticoid rhythms in the development of metabolic dysfunction.

overall_design: 3 hour corticosterone infusions (0.0035 g CORT-HBC Sigma-UK in 1mL sterile saline) delivered intravenously to adrenalectomised Sprague Dawley (male) rats, in either a pulsatile or constant pattern.    Pulsatile: 20 min infusions (at a rate of 1ml/hr) every hour (at 0-20 min, 60-80 min and 120-140 min).  Constant: constant infusion (at a rate of 0.333 ml/hr).   Dose matched hourly by rate.      ChIP-Seq: Liver samples collected at 140 min and 180 min for both infusion patterns; corresponding to the 3rd pulse peak and nadir of the pulsatile infusion respectivly. Corticosterone treated samples were compared to pulsatile vehicle infusions (control tissue) collected at 140 min and 180 min. Separate ChIP assays conducted with antibodies for the glucocorticoid receptor or pSer2 RNA polymerase II (phosphorylated serine 2 residue within the carboxy terminal domain) and sequenced. For each ChIP-seq replicate/condition/timepoint, liver samples from 6 rats were collected (72 rats in total). From each replicate/condition/timepoint, 10 x 100ug chromatin aliquots were prepared and immunoprecipitated with antibodies to either GR or pSer2 Pol2 before being pooled to prepare a separate library for each replicate/condition/timepoint/antibody. Note: Two separate ChIP-seq experiments were performed independently to allow for concordant peak calling analysis.    RNA-Seq: Liver samples collected at 180 min for both infusion patterns. Pulsatile corticosterone infusion compared to pulsatile vehicle infusion samples, and constant corticosterone infusion compared to constant vehicle infusion liver samples (N=3).

first: Matthew

middle: T

last: Brinie

first: Yvonne

last: Kerhsaw

first: Audrys

last: Pauza

first: Sohyoung

first: Songjoon

last: Baek

first: Mark

last: Rogers

first: Alex

middle: R

last: Paterson

first: Diana

last: Stavreva

first: David

last: Murphy

first: Gordon

middle: L

last: Hager

first: Stafford

last: Lightman

first: Becky

last: Conway-campbell


title: Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [Bar-seq]

summary: Genetic variation that underlies phenotypic differences provides the material on which evolutionary selection acts. Gene duplication/amplification is one type of genetic variation that can allow an organism to rapidly respond to environmental changes by increasing gene dosage. While the potential benefits afforded by gene amplification during evolution are well known, there is also a significant fitness cost to increasing gene dosage including resource shortages and burdening cellular systems. Although the evolutionary importance of gene duplication has long been appreciated, little is known about natural variation in the tolerance of duplication of specific genes. To investigate this question, we expressed the same high-copy gene overexpression (OE) library in a laboratory strain and 14 different wild S. cerevisiae isolates, together representing 4 lineages and several admixed strains, to explore the natural variation in tolerance to gene OE. Our results distinguish universal effects common to many studied strains versus strain-specific effects including broad-scale and gene-specific differences in the consequences of OE.  These results raise important implications for the accessibility of evolutionary trajectories afforded by gene OE, depending on genetic background.

overall_design: We conducted a barcode sequencing experiment examining 15 yeast strains expressing a high copy number plasmid library. For each strain, we took samples at generation 0 (start of experiment) and generation 10 to quantify how plasmid abundance changes over time. Each strain was measured in biological triplicate for a total of 90 samples.

middle: P


title: Epigenomics of nasal mucosa in children with acute respiratory illness

status: Public on Apr 06 2021

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

summary: NOT PROVIDED; REQUESTED

overall_design: Pooled WGBS sequencing of nasal mucosa across the lifespan

first: Daniel

last: Louiselle

first: Nyshele

last: Posey

first: Dithi

last: Banerjee

first: Ranjaraj

last: Selvarangan

first: Tomi

last: Pastinen

first: Elin

last: Grundberg


title: Lifespan charactarization of the nasal mucosa

first: Konner

last: Winkley

address: 2401 Gillham Road

department: Genomic Medicine Center

institute: Children's Mercy Research Institute

summary: Single-cell RNA-sequencing of the nasal mucosa across the lifespan

first: Winkley

last: Konner

first: Louiselle

last: Daniel

first: Posey

last: Nyshele

first: Banerjee

last: Dithi

first: Selvarangan

last: Ranjaraj

first: Pastinen

last: Tomi

first: Grundberg

last: Elin


title: Differential DNA Methylation and Transcriptional Signatures Characterize Impairment of Progenitor Cells in Pediatric Human Muscle Contractures Following Brain Injury [array]

status: Public on Apr 02 2021

city: Chicago

first: Andrea

middle: A.

last: Domenighetti

state: IL

address: 345 East Superior St

institute: Northwestern University & Rehabilitation Institute of Chicago

summary: Limb contractures are a debilitating and progressive consequence of a wide range of pediatric conditions that affect skeletal muscles, including perinatal brain injury causing cerebral palsy (CP). While several rehabilitation therapies are currently used in the clinical setting, their long-term effectiveness in treating contractures is marginal since they do not change underlying muscle biological properties. Therefore, new therapies based on a biological understanding of contracture development are needed. Here we show that myoblast progenitor cells from contractured muscle in children with CP had higher rates of proliferation than control cells from typically developing children. This phenotype was associated with upregulation of DNMT3a and patterns of DNA hypermethylation and gene expression that favored cell expansion over quiescence. Treatment of CP progenitors with 5-azacytidine (AZA), a DNMT inhibitor and hypomethylating agent, normalized this epigenetic imprint and promoted exit from mitosis. Together with previous studies demonstrating reduction in myoblast differentiation capacity, these data suggest that mechanisms of early myofiber growth and establishment of an adult population of quiescent stem cells could be compromised in CP. Hypomethylating agents like AZA could be used to rescue myogenesis and promote muscle growth in contractured muscle and thus may represent a new approach to treating this devastating condition

overall_design: We performed DNA methylation analysis of cultured proliferating satellite cell-derived myoblast precursors from contractured cerebral palsy (CP) muscles and typically developing control (N) muscles, treated and non-treated with hypomethylating agent 5-azacytidine (AZA)

first: Ryan

last: Embry


title: Glis1 regulates gene expression in trabacular meshwork

status: Public on Apr 05 2021

city: Research Triangle Park

first: Anton

last: Jetten

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

summary: Glis1 regulates the fuctional properties of trabacular meshwork via regulating the gene expression at transcriptional level.

overall_design: Trabacular meshwork cells were knockdown and overexpressed with Glis1 expression and followed by RNA seq and ChIP seq for further analysis.

first: Chitrangda

last: Srivastava


title: Genome-wide epigenome mapping in human induced pluripotent cells in WT and KMT2CKO cells. [RNA-Seq]

status: Public on Apr 01 2021

city: St Louis

first: Todd

last: Druley

state: Missouri

address: 660 South Euclid Ave

department: Department of Pediatrics

institute: Washington University In St Louis

summary: KMT2C is a histone methyltransferase that mono-methylates lysine four at enhancer regions. This study compares the transcriptomic profile between WT and KMT2C KO cells and further evaluates their functional validation by applying the invitro hematopoietic differentiation protocol.

overall_design: Examination of transcriptomic profile in WT and KMT2C KO cells.

first: Druley

last: Todd


title: Genome-wide epigenome mapping in human induced pluripotent cells in WT and KMT2CKO cells. [ATAC-Seq]

summary: KMT2C is a histone methyltransferase that mono-methylates lysine four at enhancer regions. This study compares the open and closed chromatin region between WT and KMT2C KO cells and further evaluates their functional validation by applying the invitro hematopoietic differentiation protocol.

overall_design: Examination of open and closed chromatin region in WT and KMT2CKO hIPSCs cells.


title: Genome-wide epigenome mapping in human induced pluripotent cells in WT and KMT2CKO cells. [ChIP-Seq]

summary: KMT2C is a histone methyltransferase that mono-methylates lysine four at enhancer regions. This study compares the histone modification pattern between WT and KMT2C KO cells and further evaluates their functional validation by applying the invitro hematopoietic differentiation protocol.

overall_design: Examination of 4 different histone modifications in WT and KMT2CKO hIPSCs cells.


title: A transcription-based mechanism for oncogene-induced lethality in BRCA1/2-deficient cells [RNA-seq]

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

institute: Institut Imagine

summary: Heterozygous germline mutations in BRCA1 or BRCA2 predispose to breast, ovarian, as well as other cancers. The main physiological function of BRCA1 and BRCA2 is to facilitate DNA replication, by stabilising and re-starting stalled replication forks. Consequently, inactivation of either BRCA1 or BRCA2 genes leads to replication pathologies and accumulation of DNA double strand breaks. Similar to BRCA1/2 inactivation, oncogene overexpression interferes with replication and inflicts DNA damage. It remains unclear how the replication defects in the two settings differ from each other and what is their combined effect on cell viability. Here, we report that accumulation of β-catenin, an oncogene of the WNT signalling pathway, is synthetically lethal with BRCA1/2 inactivation. We identify two transcription-dependent mechanisms that mediate oncogene toxicity in the context of BRCA1/2 deficiency. Firstly, accumulation of β-catenin activates E2F-dependent transcription, which accelerates G1/S transition, thus counteracting the delayed S-phase entry caused by BRCA1/2 abrogation. This, in turn, triggers illegitimate origin firing leading to fork collapse, DNA damage and deregulation of gene expression. Secondly, we find that β-catenin accumulation suppresses transcription of CDKN1A gene encoding p21, a modulator of fork progression. Decreased replication rates represent a hallmark of BRCA2 deficiency. Through p21 downregulation, β-catenin accelerates replication fork progression in BRCA2-deficient cells, thereby inflicting DNA damage and triggering cell death. Thus, our results demonstrate that oncogene-driven premature S-phase entry and increased replication rate are lethal in the context of BRCA1/2 abrogation, which explains the mutual exclusivity between oncogene activation and BRCA1/2 gene mutations in human tumours.

overall_design: RNA-seq data in BRCA2-proficient or -deficient H1299 cells ±GSK3 inhibitor (LY2090314) and/or ±siβ-catenin

first: Rebecca

middle: A

last: Dagg

first: Gijs

last: Zonderland

first: Giacomo

last: Rosetti

first: Florian

last: Groelly

first: Sonia

last: Barroso

first: Eliana

last: Tacconi

first: Benjamin

last: Wright

first: Helen

last: Lockstone

first: Andres

last: Aguilera

first: Thanos

last: Halazonetis

first: Madalena

last: Tarsounas


title: A transcription-based mechanism for oncogene-induced lethality in BRCA1/2-deficient cells

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genome-wide epigenome mapping in human induced pluripotent cells in WT and KMT2CKO cells.


title: A transcription-based mechanism for oncogene-induced lethality in BRCA1/2-deficient cells [EdU-seq]

summary: Heterozygous germline mutations in BRCA1 or BRCA2 predispose to breast, ovarian, as well as other cancers. The main physiological function of BRCA1 and BRCA2 is to facilitate DNA replication, by stabilising and re-starting stalled replication forks. Consequently, inactivation of either BRCA1 or BRCA2 genes leads to replication pathologies and accumulation of DNA double strand breaks. Similar to BRCA1/2 inactivation, oncogene overexpression interferes with replication and inflicts DNA damage. It remains unclear how the replication defects in the two settings differ from each other and what is their combined effect on cell viability. Here, we report that accumulation of β-catenin, an oncogene of the WNT signalling pathway, is synthetically lethal with BRCA1/2 inactivation. We identify two transcription-dependent mechanisms that mediate oncogene toxicity in the context of BRCA1/2 deficiency. Firstly, accumulation of -catenin activates E2F-dependent transcription, which accelerates G1/S transition, thus counteracting the delayed S-phase entry caused by BRCA1/2 abrogation. This, in turn, triggers illegitimate origin firing leading to fork collapse, DNA damage and deregulation of gene expression. Secondly, we find that β-catenin accumulation suppresses transcription of CDKN1A gene encoding p21, a modulator of fork progression. Decreased replication rates represent a hallmark of BRCA2 deficiency. Through p21 downregulation, β-catenin accelerates replication fork progression in BRCA2-deficient cells, thereby inflicting DNA damage and triggering cell death. Thus, our results demonstrate that oncogene-driven premature S-phase entry and increased replication rate are lethal in the context of BRCA1/2 abrogation, which explains the mutual exclusivity between oncogene activation and BRCA1/2 gene mutations in human tumours.

overall_design: EdUseq-HU assays to monitor nascent DNA synthesis in BRCA1+/+ or BRCA1-/- RPE1 cells ±GSK3 inhibitor (LY2090314) and BRCA2-proficient or -deficient H1299 cells ±GSK3 inhibitor (LY2090314)


title: Klotho inhibits neuronal senescence in human brain organoids

status: Public on Apr 09 2021

city: St Lucia

first: Mohammed

last: Shaker

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd,, Brisbane

department: AIBN

institute: The University of Queensland

summary: We report the application of brain organoids to study cellular senescence, in particular Klotho declining in expresssion mediates neuronal senescence, bulk RNA-sequencing further identified the potenital downstream target tha may modulate cellular senescence in the brain.

overall_design: Examination of 2 sets of human brain organoids with and without Klotho overexpression at wekk 13 of in vitro culture

first: Ernst

last: Wolvetang


title: Development of a glucocorticoid exposure signature for SLE

status: Public on Mar 31 2021

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

institute: Hudson Institute of Medical Research

summary: We performed RNA-seq on peripheral blood mononuclear cells (PBMC) from healthy human donors treated with interferon alpha 2a (1000IU/mL) +/- dexamethasone 10^-7M, with the aims of studying interactions between IFN and glucocorticoid induced gene expression, as well as identifying potential transcripts that may be used as a glucocorticoid exposure signature in clinical practice in patients with SLE. Transcripts identified from RNA-seq data were analysed in SLE patient data sets to validate clinical utility. We found that dexamethasone minimally impacts on interferon stimulated gene expression however IFN altered gene transcription of many previously reported glucocorticoid induced genes.

overall_design: Examination of IFN and dexamethasone induced gene expression changes in human PBMC.

first: Linden

first: Melissa

last: Northcott

first: Eric

last: Morand


title: Soy Infant Formula Is Not Estrogenic or Results in Reproductive Toxicity in Male Piglets

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St. Slot 782

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: The current study directly compared the effects of soy formula feeding with those of estradiol or pure genistein in the neonatal piglet, an animal model which most closely resembles the human infant physiologically and in isoflavone metabolism

overall_design: Dutch Landrace Duroc piglets were fed with a diet with Soy, Sow, Milk, and Milk supplemented with estradiol  or genistein, from postnatal day 2 to 21.

first: Martin

last: Ronis

first: MKartik

last: Shankar

first: Leah

last: Hennings

first: Neha

last: Sharma

first: Michael

last: Blackburn

first: Isabelle

last: Miousee

first: Harry

last: Dawson

first: Celine

last: Chen


title: Relationship between the miRNA Profiles and Oncogene Mutations in Non-Smoker Lung Cancer. Relevance for Lung Cancer Personalized Screenings and Treatments

status: Public on Mar 25 2021

city: Genova

first: Alessandra

last: Pulliero

state: Genova

address: Via A. Pastore 1

country: Italy

institute: Dipartimento di Scienze della Salute UNIGE

summary: Oncogene mutations may be drivers of the carcinogenesis process. MicroRNA (miRNA) alterations may be adaptive or pathogenic and can have consequences only when mutation in the controlled oncogenes occurs. The aim of this research was to analyze the interplay between miRNA expression and oncogene mutation. A total of 2549 miRNAs were analyzed in cancer tissue—in surrounding normal lung tissue collected from 64 non-smoking patients and in blood plasma. Mutations in 92 hotspots of 22 oncogenes were tested in the lung cancer tissue. MicroRNA alterations were related to the mutations occurring in cancer patients. Conversely, the frequency of mutation occurrence was variable and spanned from the k-ras and p53 mutation detected in 30% of patients to 20% of patients in which no mutation was detected. The prediction of survival at a 3-year follow up did not occur for mutation analysis but was, conversely, well evident for miRNA analysis highlighting a pattern of miRNA distinguishing between survivors and death in patients 3 years before this clinical onset. A signature of six lung cancer specific miRNAs occurring both in the lungs and blood was identified. The obtained results provide evidence that the analysis of both miRNA and oncogene mutations was more informative than the oncogene mutation analysis currently performed in clinical practice.

overall_design: We explored whether the miRNA lung tumor expression profile was predictive of the clinical outcome (alive or not) in the following years after surgery

first: Alberto

last: Izzotti

first: Simona

last: Coco

first: Gabriela

last: Coronel Vargas


title: Characterization of an ex vivo equine endometrial tissue culture model using next-generation RNA-sequencing technology

status: Public on Mar 27 2021

city: Aberystwyth

first: Maithe

middle: Monteiro

last: Rocha Monteiro de Barros

state: Ceredigion

address: Penglais Campus

institute: Aberystwyth University

summary: Persistent mating-induced endometritis is a major cause of poor fertility rates in the mare. Endo-metritis can be investigated using an ex vivo equine endometrial explant system which measures uterine inflammation using prostaglandin F2α as a biomarker. However, this model has yet to un-dergo a wide-ranging assessment through transcriptomics. In this study, we assessed the tran-scriptomes of cultured endometrial explants and the optimal temporal window for their use. En-dometrium harvested immediately post-mortem from native pony mares (n=8) were sampled (0 h) and tissue explants were cultured for 24, 48 and 72 h. Tissues were stored in RNA-Later, total RNA was extracted and sequenced. Differentially expressed genes (DEGs) were defined using DESeq2 (R/Bioconductor). Principal Component Analysis indicated that the greatest changes in expression occurred in the first 24 h of culture when compared to autologous biopsies at 0 h. Fewer DEGs were seen between 24-48 h of culture suggesting the system was more stable than during the first 24 h. No genes were differentially expressed between 48 and 72 h but the low number of background gene expression suggested that explant viability was compromised after 48 h. STRING assessments of gene ontology suggested that DEGs between 24-48 h were linked to inflammation, immune system, cellular processes, environmental information processing and signal transduction. Taken together our observations indicated that 24- 48 h is the optimal temporal window when the explant model can be used. This key observation will facilitate the appropriate use of this as a model for further research into the equine endometrium and potentially the progression of mating-induced endo-metritis to persistent inflammation between 24-48 h.

overall_design: In-depth transcriptomic assessment of endometrial explants over a culture period of 72 h

first: Maithê

last: Monteiro de Barros

first: Mina

last: Davies-Morel

first: Christopher

last: Creevey

first: Luis

last: Mur

first: Roger

middle: H

last: Alison

first: Deborah

last: Nash